Spec_Tools Tutorial

This jupyter script is used as a showcase for the spec_tools toolbox, which can be used for the analysis of IR Spectra using Python.

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import altair as alt
from modules import spec_tools
from pybaselines import Baseline, utils

The Spectrum Class

The Spectrum Class is the main object of the module. An object of the spectrum class can be initialized by using the corresponding method from the class

spec_tools.Spctrum.from_csv("filepath",sep=";", comma=",")

Spectrum = spec_tools.Spectrum.from_csv("shee2.csv",sep=";",comma=",")

A simple plot of the whole spectrum can be done with the plot_spectrum function. A additional header may be given

Spectrum.plot_spectrum(title="Hello")

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

By using a loop one can extract different spectral windows out of the spectrum

spectral_windows = [[2200,2215],[2175,2190]]

spectrums = []

for window in spectral_windows:
    spectrum_window = Spectrum.split_spectral_window(window)
    spectrums.append(spectrum_window)


spectrum1 = spectrums[0]
spectrum2 = spectrums[1]

spectrum1.plot_spectrum(title="Spectrum 1")

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

The Baseline Class

Using an Instance of the Spectrum Class one can initialize the Baseline Class and fit/obtain different baselines.

For this them package pybaselines is used

Using spectrum1 we now try out different fitting procedures

Baseline1 = spec_tools.Baseline(spectrum1)

fit, params  = Baseline1.fit_baseline_asls(lam=10000,tol=1e-5,max_iter=1000)


# This Baseline now be plotted under the spectrum

Baseline1.plot_baseline_and_spectrum("Hello")

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

The baseline can now be substracted yielding a new object of the spectrum class

Spectrum1_corr = Baseline1.substract_baseline()

Spectrum1_corr.interactive_integration()

Integration using different deconvolution methods

chart, peaks = Spectrum1_corr.plot_spectrum_peak_picking(threshold = 0.001)

chart

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

# now given the chart we can initialize the Deconvole Object

Deconvolution = spec_tools.Deconvolution(Spectrum1_corr,peaks)

print(Deconvolution.peaks)

fit = Deconvolution.fit_gaussian(Deconvolution.peaks[2])

Deconvolution.plot_gaussian_fit(Deconvolution.peaks[2])

[57 81 96]

Deconvolution.fit_multiple_gaussians_and_plot(broadness=3)

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)
/opt/anaconda3/lib/python3.11/site-packages/altair/utils/core.py:395: FutureWarning: the convert_dtype parameter is deprecated and will be removed in a future version.  Do ``ser.astype(object).apply()`` instead if you want ``convert_dtype=False``.
  col = df[col_name].apply(to_list_if_array, convert_dtype=False)

# Calculate Integrals of the Fitted Functions

integrals = Deconvolution.calculate_integral_of_fits()



# Now we can plot the integrals

ratios = spec_tools.ratios_of_integrals(integrals,2)

print(ratios)
plt.bar(range(len(integrals)),integrals)
plt.show()

[0.08226189768121268, 0.4693617068585285, 1.0]

Integration using the Derivative Spectrum:

• Goal ist to find the integration boundaries for the different peaks
• For this we first generate the derivative spectrum as a object

Spectrum1_corr_derivative = Spectrum1_corr.derivative_spectrum()

Spectrum1_corr_derivative.plot_spectrum(title="Derivative")
Spectrum1_corr_derivative_2 = Spectrum1_corr_derivative.derivative_spectrum()

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

Spectrum1_corr_derivative.plot_derivative(title="Derivative")

# Obtain Peaks from second derivative

peaks = Spectrum1_corr_derivative_2.find_maxima(threshold=0.05)

print(peaks)

Spectrum1_corr_derivative_2.plot_spectrum_with_peaks(peaks)

[ 91 100  81  96]

# We can now visualize this peaks in the original spectrum

Spectrum1_corr_derivative.plot_spectrum_with_peaks(peaks)

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

Spectrum Plotting

For this the

Spectrum = spec_tools.Spectrum.from_csv("shee2.csv",sep=";",comma=",")



Spectrum.plot_spectrum(title="Hello")

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

Plot Spectral Window

By using the plot_spectral_window method, one can plot the spectral window of the spectrum

spectrum.plot_spectral_window()

Spectrum.plot_spectral_window(title="Hello",x_min=2150, x_max=2250)

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

# Perform peackpicking in spectral window

Spectrum.plot_spectral_window_peak_picking(title="Hello,",x_min=1000, x_max=2250, threshold=0.1)

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

(alt.LayerChart(...), alt.Chart(...))

chart, integral = Spectrum.calculate_integral(x_min=1000, x_max=2250)

chart

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/core.py:395: FutureWarning: the convert_dtype parameter is deprecated and will be removed in a future version.  Do ``ser.astype(object).apply()`` instead if you want ``convert_dtype=False``.
  col = df[col_name].apply(to_list_if_array, convert_dtype=False)

Plot Multiple Spectral Windows

ls_windows = [[2200,2215],[2175,2190]]
subtitles = ["Window 1", "Window 2"]

Spectrum.plot_multiple_spectral_windows(ls_of_windows=ls_windows, title="Nice Shit",subtitles=subtitles)

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

# Calculate Integral of Multiple peaks

chart, areas = Spectrum.integrate_multiple_spectral_windows(ls_of_windows=ls_windows)

chart

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)
/opt/anaconda3/lib/python3.11/site-packages/altair/utils/core.py:395: FutureWarning: the convert_dtype parameter is deprecated and will be removed in a future version.  Do ``ser.astype(object).apply()`` instead if you want ``convert_dtype=False``.
  col = df[col_name].apply(to_list_if_array, convert_dtype=False)
/opt/anaconda3/lib/python3.11/site-packages/altair/utils/core.py:395: FutureWarning: the convert_dtype parameter is deprecated and will be removed in a future version.  Do ``ser.astype(object).apply()`` instead if you want ``convert_dtype=False``.
  col = df[col_name].apply(to_list_if_array, convert_dtype=False)

Spectrum.plot_derivative(title="Hello")

/opt/anaconda3/lib/python3.11/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'add_selection' is deprecated. Use 'add_params' instead.
  warnings.warn(message, AltairDeprecationWarning, stacklevel=1)

Baseline Correction

Baseline = spec_tools.Baseline(Spectrum)

Baseline.fit_baseline_asls(lam=5e6, tol=1e-3, max_iter=20)

(array([ 0.01110359,  0.01110664,  0.0111097 , ..., -0.0405984 ,
        -0.04062492, -0.04065144]),
 {'weights': array([0.01, 0.01, 0.01, ..., 0.01, 0.01, 0.01]),
  'tol_history': array([0.68991331, 0.72181646, 0.71097111, 0.61806805, 0.48002348,
         0.34684309, 0.25761441, 0.26805353, 0.17193777, 0.11523654,
         0.06436087, 0.01562341, 0.        ])})